Directory SEQ_QUALITY/

Directory Created:
2003-07-16 17:14
Total Files:
12
Deleted Files:
10
Lines of Code:
2459

[root]/SEQ_QUALITY

Lines of Code

SEQ_QUALITY/ Lines of Code

Developers

Author Changes Lines of Code Lines per Change
Totals 555 (100.0%) 13734 (100.0%) 24.7
huberj 236 (42.5%) 5977 (43.5%) 25.3
baderk 87 (15.7%) 5241 (38.2%) 60.2
westram 232 (41.8%) 2516 (18.3%) 10.8

Most Recent Commits

westram 2019-04-01 17:41 Rev.: 17724


* partial merge from 'fts' into 'trunk'
- {{{ConfigMapping}}}:
* cleanup
* add missing tests
* fix config bug: trailing backslash at end of values did cause wrong read of data
* adds: log:branches/fts@17718:17723

2 lines of code changed in 1 file:

  • SEQ_QUALITY: Makefile (+2)
westram 2018-07-23 16:52 Rev.: 17262


* partial merge from 'group' into 'trunk'
- fixes to arb_progress
* adds:
- log:branches/group@17191:17218,17220:17260
- log:branches/progress@17195:17216,17218:17259

6 lines of code changed in 3 files:

  • SEQ_QUALITY: SQ_functions.cxx (-5), SQ_functions.h (-2), SQ_main.cxx (+6 -1)
westram 2018-06-15 13:08 Rev.: 17110


* reintegrates 'tree' into 'trunk'
- implements #735
* adds:
- log:branches/addtest@17040:17044
- log:branches/tree@16921:17109

4 lines of code changed in 2 files:

  • SEQ_QUALITY: SQ_functions.cxx (+3 -3), SQ_main.cxx (+1 -1)
westram 2017-11-28 19:22 Rev.: 16766


* reintegrates 'gcc' into 'trunk'
- mostly cosmetics changes
* adds: log:branches/gcc@16655,16741:16743,16752:16765

4 lines of code changed in 2 files:

  • SEQ_QUALITY: SQ_GroupData.h (+3 -3), SQ_helix.h (+1 -2)
westram 2017-11-28 18:09 Rev.: 16763


* partial merge from 'gcc' into 'trunk'
- use {{{nullptr}}} in Cxx11 (with backward compatibility)
* adds: log:branches/gcc@16683:16740,16744:16746,16751

33 lines of code changed in 5 files:

  • SEQ_QUALITY: SQ_GroupData.h (+1 -1), SQ_ambiguities.h (+4 -4), SQ_functions.cxx (+15 -15), SQ_helix.h (+7 -7), SQ_main.cxx (+6 -6)
westram 2017-11-06 14:54 Rev.: 16628


* reintegrates 'vectorize' into 'trunk'
- fixes #700
* documented vectorization-checks
* fine-grained check based on gcc-version
- drops old gcc-versions (<4.4.3)
- new attribute {{{__ATTR__DONT_VECTORIZE}}}
* disabled vectorization of {{{POS_TREE2::init_static()}}} for newer gcc-versions (generated code fails tests)
- added a bunch of new vectorization-checks (probably irrelevant to overall performance)
* adds: log:branches/vectorize@15531:16585,16595:16627

2 lines of code changed in 1 file:

  • SEQ_QUALITY: SQ_GroupData.h (+2 -2)
westram 2017-07-10 12:29 Rev.: 16119


* reintegrates 'saiexport' into 'trunk'
- implements #743
* adds: log:branches/saiexport@16023:16118

4 lines of code changed in 1 file:

  • SEQ_QUALITY: SQ_functions.cxx (+4 -1)
westram 2017-01-04 18:06 Rev.: 15513


* reintegrates 'warnings' into 'trunk'
- activate additional warnings (gcc 5.x++)
- Cxx11-forward final (classes+methods)
- fix tag problems caused by using preprocessor
* adds: log:branches/warnings@15486:15489,15491:15501,15506:15512

1 lines of code changed in 1 file:

  • SEQ_QUALITY: SQ_GroupData.h (+1 -1)
westram 2016-08-17 20:39 Rev.: 15198


* remove {{{virtual}}} if {{{OVERRIDE}}} is present
- OVERRIDE implies 'implicit virtual' (if code compiles as C++11 <- tested on build server!)

1 lines of code changed in 1 file:

  • SEQ_QUALITY: SQ_GroupData.h (+1 -1)
westram 2016-08-11 11:05 Rev.: 15176


* reintegrates 'fixres' into 'trunk'
- fixes #715
* adds: log:branches/fixres@15127:15175

4 lines of code changed in 2 files:

  • SEQ_QUALITY: Makefile (+3), SQ_functions.cxx (+1 -1)
westram 2016-07-14 14:45 Rev.: 15053


* merge most WINDOW patches from 'color' into 'trunk'
- color-ranges (completes implementation of #682)
* new types (cyclic, planar and spatial)
* can display as canvas-overlay
* setup in separate window
* allow external access via ID (query, activate)
* adds: log:branches/color@14984,14986:14987,14989,14993,15000,15005:15006,15008,15011,15036

1 lines of code changed in 1 file:

  • SEQ_QUALITY: Makefile (+1)
westram 2016-04-16 14:52 Rev.: 14731


* mark code binding callbacks to non-button-widgets (probably incomplete; see #559 for details)

1 lines of code changed in 1 file:

  • SEQ_QUALITY: SQ_GroupData.cxx (+1 -1)
westram 2015-11-04 10:57 Rev.: 14453


* do not cast AW_POPDOWN

1 lines of code changed in 1 file:

  • SEQ_QUALITY: SQ_main.cxx (+1 -1)
westram 2015-10-28 19:12 Rev.: 14434


* use typed callbacks in AWTI, PRIMER_DESIGN, SEQ_QUALITY and REFENTRIES

7 lines of code changed in 1 file:

  • SEQ_QUALITY: SQ_main.cxx (+7 -8)
westram 2015-07-31 16:15 Rev.: 14118


* added {{{awt_create_filter_awars}}}
- made all awars 'tmp' (saving them did not work)

19 lines of code changed in 1 file:

  • SEQ_QUALITY: SQ_main.cxx (+19 -24)
westram 2015-04-11 11:10 Rev.: 13705


* add config-manager to sequence quality

23 lines of code changed in 2 files:

  • SEQ_QUALITY: Makefile (+1), SQ_main.cxx (+22 -3)
westram 2015-03-29 12:47 Rev.: 13625


* reintegrates 'pars' into 'trunk'
- fixes #528, #609, #620, #631, #633, #640, #641
- implements #619, #627
* adds:
- log:branches/addtest@13123:13260,13523:13551,13570
- log:branches/check@13365:13375,13450:13457
- log:branches/check2@13458:13465
- log:branches/fix@13522:13588
- log:branches/fixres@13270:13277,13279:13293,13295:13326
- log:branches/pars@12938:13280,13282:13325,13327:13387,13389:13527,13530:13624

27 lines of code changed in 4 files:

  • SEQ_QUALITY: Makefile (+2), SQ_functions.cxx (+16 -16), SQ_functions.h (+4 -5), SQ_main.cxx (+5 -4)
westram 2015-01-23 15:19 Rev.: 13443


* reintegrates 'vectorize' into 'trunk'
- adds vectorization check for gcc 4.9.x / NDEBUG compile
* adds:
- log:branches/vectorize@13428:13442

1 lines of code changed in 1 file:

  • SEQ_QUALITY: Makefile (+1 -1)
westram 2014-08-14 12:18 Rev.: 12757


* unify selectionlist creator names
* awt_create_selection_list_on_pt_servers
- remove param 'popup', instead split into two function (button and list) as done for SAIs

1 lines of code changed in 1 file:

  • SEQ_QUALITY: SQ_main.cxx (+1 -1)
westram 2014-05-13 10:49 Rev.: 12225


* pass 'fallback2default' down into awt_create_selection_list_on_trees()

1 lines of code changed in 1 file:

  • SEQ_QUALITY: SQ_main.cxx (+1 -1)
westram 2014-04-30 14:36 Rev.: 12138


* reintegrates 'fix' into 'trunk'
- fixes #522
* adds:
- log:branches/fix@12058:12137

52 lines of code changed in 1 file:

  • SEQ_QUALITY: SQ_main.cxx (+52 -49)
westram 2014-01-28 18:13 Rev.: 11512


* merge [11502,11504,11505] from 'dist' into 'trunk'
* adds:
- log:branches/dist@11502,11504:11505

4 lines of code changed in 2 files:

  • SEQ_QUALITY: SQ_main.cxx (+3 -4), seq_quality.h (+1 -1)
westram 2013-12-26 13:48 Rev.: 11401


* reintegrates 'tree' into 'trunk':
- consensus trees:
* support for merging partial trees ("worked" before, but results were crap; implements #65)
* generated trees are automatically re-rooted and -ordered
* always list source trees in consensus-tree-comment; show info about partial trees
* fixed progress bar
- made GBT_TREE a base class of other tree classes (implements #31)
- save tree properties in properties (not in DB)
- new functions 'Remove zombies/marked from ALL trees'
- tree load/save: layout fixes
- unit tests
* added tests for basic tree modifications (PARSIMONY)
- performance:
* compute_tree updates tree information in one traversal
* tree generators are now capable to generate any type of tree (w/o needing to copy it once)
- bugfixes:
* NNI (of marked species) was also always performed for colored species
* centered beautify-order is stable now
* improved 'search optimal root'
* adds:
- log:branches/tree@10500:10534,10542:11182,11184:11186,11188:11400
- log:branches/treeTests@11198:11335

3 lines of code changed in 1 file:

  • SEQ_QUALITY: SQ_main.cxx (+3 -5)
westram 2013-11-29 10:32 Rev.: 11261


* use awt_create_select_filter_win() as typed callback
* removed superfluous struct keyword
* renamed some variables ('cd'-ex)

3 lines of code changed in 1 file:

  • SEQ_QUALITY: SQ_main.cxx (+3 -3)
westram 2013-11-27 19:55 Rev.: 11248


- need cb.h in awt_sel_boxes.hxx

0 lines of code changed in 1 file:

  • SEQ_QUALITY: SQ_main.cxx (-1)
westram 2013-11-02 17:41 Rev.: 11034


* depends for [11033]

2 lines of code changed in 1 file:

  • SEQ_QUALITY: Makefile (+2)
westram 2013-10-31 18:14 Rev.: 11007


* prototype for GBK_terminate differed between arb_core.h and arb_msg.h

1 lines of code changed in 1 file:

  • SEQ_QUALITY: Makefile (+1)
westram 2013-10-31 16:40 Rev.: 11002


* 'class { public' -> struct

33 lines of code changed in 3 files:

  • SEQ_QUALITY: SQ_GroupData.h (+8 -7), SQ_helix.h (+15 -15), SQ_physical_layout.h (+10 -10)
westram 2013-10-31 15:10 Rev.: 10996


* use cflags before cxxflags

1 lines of code changed in 1 file:

  • SEQ_QUALITY: Makefile (+1 -1)
westram 2013-10-30 16:58 Rev.: 10974


* renamed include variables

1 lines of code changed in 1 file:

  • SEQ_QUALITY: Makefile (+1 -1)
westram 2013-10-29 13:55 Rev.: 10956


* made A_CC and A_CXX consistent
- A_CXX previously contained cxxflags
- cxxflags are now passed down and used separately

1 lines of code changed in 1 file:

  • SEQ_QUALITY: Makefile (+1 -1)
westram 2013-10-29 13:23 Rev.: 10955


- renamed
* ACC -> A_CC
* CPP -> A_CXX (misleading atm, since it contains c++flags)

1 lines of code changed in 1 file:

  • SEQ_QUALITY: Makefile (+1 -1)
westram 2013-10-29 12:43 Rev.: 10954


- document mechanism used by ARB to export variables to submakefiles
- document most important variables

1 lines of code changed in 1 file:

  • SEQ_QUALITY: Makefile (+1 -1)
westram 2013-10-21 14:16 Rev.: 10863


* replaced usage of untyped AW_POPUP_HELP

1 lines of code changed in 1 file:

  • SEQ_QUALITY: SQ_main.cxx (+1 -1)
westram 2013-09-09 16:36 Rev.: 10563


- include downcast.h from arbdbt.h
(this break C++11 compilation, i.e. gcc4.8 or newer)[[BR]]
amendment:
* also broke compilation on ubuntu 13.04 and with gcc 4.7.3 (due to nameclash with boost)

2 lines of code changed in 1 file:

  • SEQ_QUALITY: Makefile (+2)
westram 2013-07-16 12:45 Rev.: 10280


* GBT_delete_tree
- expects *& as param (value is set to NULL after delete)
- accept NULL as input

1 lines of code changed in 1 file:

  • SEQ_QUALITY: SQ_main.cxx (+1 -1)
westram 2013-07-04 16:49 Rev.: 10212


* depends for recent patches

7 lines of code changed in 1 file:

  • SEQ_QUALITY: Makefile (+7)
westram 2013-06-04 15:20 Rev.: 10113


* changed dynamic value-initializations into default-initializations
- i believe/know they were used with ignorance of [http://stackoverflow.com/questions/620137/do-the-parentheses-after-the-type-name-make-a-difference-with-new?answertab=active#tab-top ctor-behavior].

2 lines of code changed in 1 file:

  • SEQ_QUALITY: SQ_functions.cxx (+2 -2)
westram 2013-02-13 13:24 Rev.: 9575


- effect of [9574] (comments only)

1 lines of code changed in 1 file:

  • SEQ_QUALITY: Makefile (+1 -1)
westram 2013-02-11 12:35 Rev.: 9533


* use explicit override
- rest

13 lines of code changed in 1 file:

  • SEQ_QUALITY: SQ_GroupData.h (+13 -14)

(215 more)

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